Accurate, high-resolution sample inference from amplicon sequencing data

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Documentation for package ‘dada2’ version 1.10.0

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dada2-package DADA2 package
addSpecies Add species-level annotation to a taxonomic table.
assignSpecies Taxonomic assignment to the species level by exact matching.
assignTaxonomy Classifies sequences against reference training dataset.
c-method Change concatenation to list construction.
c-method Change concatenation to list construction.
collapseNoMismatch Combine together sequences that are identical up to shifts and/or length.
dada High resolution sample inference from amplicon data.
dada-class The object class returned by 'dada'
derep-class A class representing dereplicated sequences
derepFastq Read in and dereplicate a fastq file.
errBalancedF An empirical error matrix.
errBalancedR An empirical error matrix.
errExtremeF An empirical error matrix.
errExtremeR An empirical error matrix.
errHmpF An empirical error matrix.
errHmpR An empirical error matrix.
fastqFilter Filter and trim a fastq file.
fastqPairedFilter Filters and trims paired forward and reverse fastq files.
filterAndTrim Filter and trim fastq file(s).
getDadaOpt Get DADA options
getErrors Extract already computed error rates.
getSequences Get vector of sequences from input object.
getUniques Get the uniques-vector from the input object.
inflateErr Inflates an error rate matrix by a specified factor, while accounting for saturation.
isBimera Determine if input sequence is a bimera of putative parent sequences.
isBimeraDenovo Identify bimeras from collections of unique sequences.
isBimeraDenovoTable Identify bimeras in a sequence table.
isPhiX Determine if input sequence(s) match the phiX genome.
isShiftDenovo Identify sequences that are identical to a more abundant sequence up to an overall shift.
learnErrors Learns the error rates from an input list, or vector, of file names or a list of 'derep-class' objects.
loessErrfun Use a loess fit to estimate error rates from transition counts.
makeSequenceTable Construct a sample-by-sequence observation matrix.
mergePairs Merge denoised forward and reverse reads.
mergePairsByID Merge forward and reverse reads after DADA denoising, even if reads were not originally ordered together.
mergeSequenceTables Merge two or more sample-by-sequence observation matrices.
names<--method Deactivate renaming of dada-class objects.
names<--method Deactivate renaming of derep-class objects.
noqualErrfun Estimate error rates for each type of transition while ignoring quality scores.
nwalign Needleman-Wunsch alignment.
nwhamming Hamming distance after Needlman-Wunsch alignment.
PacBioErrfun Estimate error rates from transition counts in PacBio CCS data.
plotErrors Plot observed and estimated error rates.
plotQualityProfile Plot quality profile of a fastq file.
removeBimeraDenovo Remove bimeras from collections of unique sequences.
seqComplexity Determine if input sequence(s) are low complexity.
setDadaOpt Set DADA options
show-method method extensions to show for dada2 objects.
tperr1 An empirical error matrix.
uniques-vector The named integer vector format used to represent collections of unique DNA sequences.
uniquesToFasta Write a uniques vector to a FASTA file
writeFasta-method Writes a named character vector of DNA sequences to a fasta file. Values are the sequences, and names are used for the id lines.